No. It isn't measuring the temperature of the pad - it is controlling the temperature of the pad. If there are other things that could interfere with this (urine, your snake, substrate, etc), then it can not do its job effectively. This is why the probe placement is recommended where it has been recommended.
Yes. You should be measuring the temp of the substrate (most importantly, the surface of the glass immediately above the pad) - infrared thermometers tend to be the most efficient. From this measurement, you can choose to increase or decrease the set point of your thermostat accordingly.
Does this clarification make sense?